AlignACE version 2.2  July 7, 1998
/home/amcguire/bin/alignACE -i227_rna_methyltransferase_pyro_reg_100.orf -o227_pyro_100.ace -a/home/amcguire/genomes/ORF_pyro.txt -z/home/amcguire/genomes/pyro.fna -g0.42 -x5 -e 
Parameter values:
 expect =  	5
 ncols =   	10
 npass =   	1000
 maxnpass =	100
 nruns =   	1000
 maxnruns =	100
 repeat =  	15
 maxreps = 	3
 nread =   	500
 ncycles = 	1
 fragment =	1
 psfact =  	0.1
 gcback =  	0.42
 maxlen =  	30
 weight =  	0.8
 exclude = 	1

Input sequences:
#1	RPH00468	128	Pyrococcus_OT3

Motif number 1

AGAAGGTAAATTCTTTTTGGTGATGAAGA 	1	10	0	TTCTTTTTGG	    0.988842	-119
AAGAATTTACCTTCTTTAGGTATTTAAAGC	1	25	1	CTTCTTTAGG	    0.980795	-104
TATTTAAAGCTTGCTTTTGGCTTGAGGTTT	1	45	1	TTGCTTTTGG	    0.996052	-84
TATTAGGATGTCGGTTTTGGCAACTATGAA	1	73	0	TCGGTTTTGG	    0.984063	-56
CATCCAGGAATTTTATTAGGATGTCGGTTT	1	86	0	TTTTATTAGG	    0.957156	-43
          **********

Masking position 6
Map Score:   5.42561

Number of sites scoring better than the average of aligned sites = 128
Number in coding regions = 105
Number in noncoding regions = 23
Number of orfs with sites within 600 bp upstream = 26
Fraction of orfs with sites within 600 bp upstream = 0.00417604


Motif number 2

         TCTTCATCACCAAAAAGAATT	1	2	1	CTTCATCACC	    0.990922	-127
ACCAAAAAGAATTTACCTTCTTTAGGTATT	1	19	1	ATTTACCTTC	    0.978572	-110
TCACCTCCTTAATCTCCATCCAGGAATTTT	1	102	0	AATCTCCATC	    0.966004	-27
     TCACCCTTCACCTCCTTAATCTCCA	1	114	0	CTTCACCTCC	    0.997702	-15
          **********

Masking position 3
Map Score:   2.77301

Number of sites scoring better than the average of aligned sites = 522
Number in coding regions = 458
Number in noncoding regions = 64
Number of orfs with sites within 600 bp upstream = 76
Fraction of orfs with sites within 600 bp upstream = 0.0122069


Motif number 3

CATCACCAAAAAGAATTTACCTTCTTTAGG	1	15	1	AAGAATTTAC	    0.936182	-114
TACCTTCTTTAGGTATTTAAAGCTTGCTTT	1	32	1	AGGTATTTAA	     0.99006	-97
TTTTGGCTTGAGGTTTCATAGTTGCCAAAA	1	59	1	AGGTTTCATA	    0.901512	-70
ATCTCCATCCAGGAATTTTATTAGGATGTC	1	91	0	AGGAATTTTA	    0.989967	-38
          **********

Masking position 6
Map Score:   0.441311

Number of sites scoring better than the average of aligned sites = 356
Number in coding regions = 301
Number in noncoding regions = 55
Number of orfs with sites within 600 bp upstream = 72
Fraction of orfs with sites within 600 bp upstream = 0.0115644


Motif number 4

          **********

No masking
Map Score:   -1.89414e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 5

          **********

No masking
Map Score:   -1.89414e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0


Motif number 6

          **********

No masking
Map Score:   -1.89414e-13

Number of sites scoring better than the average of aligned sites = 0
Number in coding regions = 0
Number in noncoding regions = 0
Number of orfs with sites within 600 bp upstream = 0
Fraction of orfs with sites within 600 bp upstream = 0